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- PDB-23ri: l-alanoyl-d-glutamate peptidase bacteriophage RB49 comlpex with Zn2+ -

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Basic information

Entry
Database: PDB / ID: 23ri
Titlel-alanoyl-d-glutamate peptidase bacteriophage RB49 comlpex with Zn2+
ComponentsPeptidase M15C domain-containing protein
KeywordsANTIMICROBIAL PROTEIN / l-alanoyl-d-glutamate peptidase / bacteriophage RB49 / endolysin / Zn2+ containing form
Function / homologyPeptidase M15C / D-alanyl-D-alanine carboxypeptidase / Hedgehog signalling/DD-peptidase zinc-binding domain superfamily / peptidase activity / Peptidase M15C domain-containing protein
Function and homology information
Biological speciesEscherichia phage RB49 (virus)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsProkhorov, D.A. / Mikoulinskaia, G.V.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Other government Russian Federation
CitationJournal: To Be Published
Title: Spatial structure of L-alanoyl-D-glutamate peptidase of bacteriophage RB49
Authors: Prokhorov, D.A. / Mikoulinskaia, G.V.
History
DepositionFeb 13, 2026Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 25, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptidase M15C domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8452
Polymers14,7801
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violations
RepresentativeModel #1target function

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Components

#1: Protein Peptidase M15C domain-containing protein / l-alanoyl-d-glutamate peptidase (endolysin) bacteriophage RB49


Mass: 14780.025 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Zn2+ containing form. / Source: (gene. exp.) Escherichia phage RB49 (virus) / Gene: RB49ORF102c / Production host: Escherichia coli B (bacteria) / References: UniProt: Q7Y3Q4
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
171isotropic12D 1H-13C HSQC-ali
161isotropic13D BEST TROSY HN(CA)CB
151isotropic13D BEST TROSY HN(CO)CACB
141isotropic13D BEST TROSY HNCO
131isotropic13D BEST TROSY HN(CA)CO
121isotropic13D BEST TROSY (H)N(COCA)NH
181isotropic13D H(C)CH-TOCSY ali
1121isotropic13D (H)CCH-TOCSY ali
1111isotropic13D TROSY-(H)CCH-COSY aro
1101isotropic12D (Hb)Cb(CgCC-TOCSY)Har
191isotropic13D 1H-15N TOCSY
1151isotropic13D 1H-13C NOESY aliphatic
1141isotropic13D 1H-13C NOESY aromatic
1131isotropic13D 1H-15N NOESY

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Sample preparation

DetailsType: solution
Contents: 0.8 mM [U-100% 13C; U-100% 15N] l-alanoyl-d-glutamate peptidase, 25 mM [U-100% 2H] sodium acetate, 1 mM Zn(NO3)2, 0.03 % w/w sodium azide, 90% H2O/10% D2O
Label: endo_RB49 - Zn2+ / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMl-alanoyl-d-glutamate peptidase[U-100% 13C; U-100% 15N]1
25 mMsodium acetate[U-100% 2H]1
1 mMZn(NO3)2natural abundance1
0.03 % w/wsodium azidenatural abundance1
Sample conditionsIonic strength: 28 mM / Ionic strength err: 1 / Label: conditions_1 / pH: 4.05 / PH err: 0.05 / Pressure: AMBIENT Pa / Temperature: 298 K / Temperature err: 0.2

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 600 MHz / Details: TXI probehead

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure calculation
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
CARARelease: 1.8.4.2Keller and Wuthrichchemical shift assignment
TopSpin2.1Bruker Biospinprocessing
TopSpin2.1Bruker Biospinpeak picking
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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